A new method for handling missing species in diversification analysis applicable to randomly or nonrandomly sampled phylogenies

Systematic Biology

Volumn 61, Issue 5, 2012, Pages 785-792

  Cusimano, Natalie ^a   Stadler, Tanja ^b   Renner, Susanne S ^a  

^a UNIVERSITY OF MUNICH   (Germany)

^b ETH ZURICH   (Switzerland)

Author keywords

statistic; Birth death likelihood analysis; diversification rates; missing species problem; model fitting; nonrandom species sampling

Indexed keywords

VEGETABLE PROTEIN;

ARACEAE; ARTICLE; CELL NUCLEUS; CLASSIFICATION; COMPUTER SIMULATION; EVALUATION; GENETICS; METHODOLOGY; MOLECULAR EVOLUTION; PHYLOGENY; SOUTHEAST ASIA; SOUTHERN EUROPE;

ARACEAE; ASIA, SOUTHEASTERN; CELL NUCLEUS; CLASSIFICATION; COMPUTER SIMULATION; EVOLUTION, MOLECULAR; MEDITERRANEAN REGION; PHYLOGENY; PLANT PROTEINS;

EID: 84861212667     PISSN: 10635157     EISSN: 1076836X     Source Type: Journal    
DOI: 10.1093/sysbio/sys031     Document Type: Article

References (37)

1. Baldwin B.G., Sanderson M.J. 1998. Age and rate of diversifcation of the Hawaiian silversword alliance (Compositae). Proc. Natl. Acad. Sci. U.S.A. 95:9402-9406.
2. Barraclough T.G., Vogler A.P. 2002. Recent diversifcation rates in North American tiger beetles estimated from a dated mtDNA phy-logenetic tree. Mol. Biol. Evol. 19:1706-1716.
3. Brock C.D., Harmon L.J., Alfaro M.E. 2011. Testing for temporal variation in diversifcation rates when sampling is incomplete and non-random. Syst. Biol. 60:410-419.
4. Cusimano N., Barrett M., Hetterscheid W.L.A., Renner S.S. 2010. A phylogeny of the Areae (Araceae) implies that Typhonium, Sauro-matum and Lazarum are distinct clades. Taxon. 59:439-447.
5. Cusimano N., Bogner J., Mayo S.J., Boyce P.C., Wong S.Y., Hesse M., Hetterscheidt W.L.A., Keating R.C., French J.C. 2011. Relationships within the Araceae: comparisons of morphological patterns with molecular phylogenies. Am. J. Bot. 98:654-668.
6. Cusimano N., Renner S.S. 2010. Slowdowns from real phylogenies may not be real. Syst. Biol. 59:458-464.
7. Day J.J., Cotton J.A., Barraclough T.G. 2008. Tempo and mode of diver-sifcation of Lake Tanganyika Cichlid Fishes. PLoS One. 3:e1730.
8. Drummond A.J., Ho S.Y.W., Phillips M.J., Rambaut A. 2006. Relaxed phylogenetics and dating with confdence. PLoS Biol. 4:e88.
9. Drummond A.J., Rambaut A. 2007. Bayesian evolutionary analysis by sampling trees. BMC Evol. Biol. 7:214.
10. Gernhard T. 2008. The conditioned reconstructed process. J. Theor. Biol. 253:769-778.
11. Hartmann K., Wong D., Stadler T. 2010. Sampling trees from evolutionary models. Syst. Biol. 59:465-476.
12. Harvey P.H., May R.M., Nee S. 1994. Phylogenies without fossils Evolution. 48:523-529.
13. Hey J. 1992. Using phylogenetic trees to study speciation and extinction. Evolution. 46:627-640.
14. Höhna S., Stadler T., Ronquist F., Britton T. 2011. Inferring speciation and extinction rates under different sampling schemes. Mol. Biol. Evol. 28:2577-2589.
15. Magallón S., Sanderson M.J. 2001. Absolute diversifcation rates in angiosperm clades. Evolution. 55:1762-1780.
16. McPeek M.A. 2008. The ecological dynamics of clade diversifcation and community assembly. Am. Nat. 172:E270-E284.
17. Nakagawa S., Freckleton R.P. 2008. Missing inaction: the danger of ignoring missing data. Trends Ecol. Evol. 23:592-596.
18. Nee S. 2006. Birth-death models in macroevolution. Annu. Rev. Ecol. Syst. 37:1-17.
19. Nee S., Mooers A.O., Harvey P.H. 1992. Tempo and mode of evolution revealed from molecular phylogenies. Proc. Natl. Acad. Sci. U.S.A. 89:8322-8326.
20. Nylander J.A.A., Wilgenbusch J.C., Warren D.L., Swofford D.L. 2008. AWTY (are we there yet?): a system for graphical exploration of MCMC convergence in Bayesian phylogenetics. Bioinformatics. 24:581-583.
21. Paradis E. 1997. Assessing temporal variations in diversifcation rates from phylogenies: estimation and hypothesis testing. Proc. R. Soc. Lond. B Biol. Sci. 264:1141-1147.
22. Paradis E. 1998. Detecting shifts in diversifcation rates without fossils. Am. Nat. 152:176-187.
23. Phillimore A.B., Price T.D. 2008. Density-dependent cladogenesis in birds. PLoS Biol. 6:483-489.
24. Purvis A., Nee S., Harvey P.H. 1995. Macroevolutionary inferences from primate phylogeny. Proc. R. Soc. Lond. B Biol. Sci. 260: 329-333.
25. Pybus O.G., Harvey P.H. 2000. Testing macro-evolutionary models using incomplete molecular phylogenies. Proc. R. Soc. Lond. B Biol. Sci. 267:2267-2272.
26. Rabosky D. L. 2006a. LASER: a maximum likelihood toolkit for inferring temporal shifts in diversifcation rates. Evol. Bioinform. Online. 2:257-260.
27. Rabosky D.L. 2006b. Likelihood methods for detecting temporal shifts in diversifcation rates. Evolution. 60:1152-1164.
28. Rabosky D.L., Donnellan S.C. Talaba A.L., Lovette I.J. 2007. Exceptional among-lineage variation in diversifcation rates during the radiation of Australia's most diverse vertebrate clade. Proc. R. Soc. Lond. B Biol. Sci. 274:2915-2923.
29. R Developmental Core Team. 2006. A language and environment for statistical computing. Vienna (Austria): R Foundation for Statistical Computing.
30. Renner S.S., Zhang L.-B. 2004. Biogeography of the Pistia clade (Araceae): based on chloroplast and mitochondrial DNA sequences and Bayesian divergence time inference. Syst. Biol. 53:422-432.
31. Sanderson M.J., Bharathan G. 1993. Does cladistic information affect inferences about branching rates? Syst. Biol. 42:1-17.
32. Sanderson M.J., Donoghue M.J. 1994. Shifts in diversifcation rate with the origin of angiosperms. Science. 264:1590-1593.
33. Stadler T. 2008. Lineage-through-time plots of neutral models for speciation. Math. Biosci. 216:163-171.
34. Stadler T. 2009. On incomplete sampling under birth-death models and connections to the sampling-based coalescent. J. Theor. Biol. 261:58-66.
35. Stadler T. 2011a. Mammalian phylogeny reveals recent diversifcation rate shifts. Proc. Natl. Acad. Sci. U.S.A. 108:6187-6192.
36. Stadler T. 2011b. Simulating trees on a fxed number of extant species. Syst. Biol. 60:676-684.
37. Stadler T., Bokma F. In review. Estimating speciation and extinction rates for phylogenies of higher taxa.